7-10241816-G-T

Variant names:

• chr7-10241816-G-T
• rs7785107

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.116 in 151,712 control chromosomes in the GnomAD database, including 1,896 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17579 AN: 151594 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0344

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0835

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.116 AC: 17602 AN: 151712 Hom.: 1896 Cov.: 32 AF XY: 0.114 AC XY: 8443 AN XY: 74186

African (AFR) AF: 0.285 AC: 11793 AN: 41396

American (AMR) AF: 0.0420 AC: 638 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0344 AC: 119 AN: 3456

East Asian (EAS) AF: 0.0613 AC: 314 AN: 5126

South Asian (SAS) AF: 0.0807 AC: 389 AN: 4822

European-Finnish (FIN) AF: 0.0578 AC: 610 AN: 10558

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3349 AN: 67834

Other (OTH) AF: 0.0826 AC: 174 AN: 2106

Alfa AF: 0.0533 Hom.: 228

Bravo AF: 0.121

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.0
DANN	Benign	0.70
PhyloP100		0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7785107; hg19: chr7-10281443;